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<html><head><title>Python: module controller</title>
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<font color="#ffffff" face="helvetica, arial">&nbsp;<br><big><big><strong>controller</strong></big></big></font></td
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><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:/home/lc6/pygenome/src/controller.py">/home/lc6/pygenome/src/controller.py</a></font></td></tr></table>
    <p><tt>Controller&nbsp;module</tt></p>
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<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#fffff" face="helvetica, arial"><big><strong>Modules</strong></big></font></td></tr>
    
<tr><td bgcolor="#aa55cc"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="view.draw.html">view.draw</a><br>
</td><td width="25%" valign=top><a href="logging.html">logging</a><br>
</td><td width="25%" valign=top><a href="os.html">os</a><br>
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<font color="#ffffff" face="helvetica, arial"><big><strong>Classes</strong></big></font></td></tr>
    
<tr><td bgcolor="#ee77aa"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
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<dt><font face="helvetica, arial"><a href="__builtin__.html#object">__builtin__.object</a>
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<dt><font face="helvetica, arial"><a href="controller.html#MainWindowController">MainWindowController</a>
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<font color="#000000" face="helvetica, arial"><a name="MainWindowController">class <strong>MainWindowController</strong></a>(<a href="__builtin__.html#object">__builtin__.object</a>)</font></td></tr>
    
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<td colspan=2><tt>Controller&nbsp;for&nbsp;main&nbsp;window<br>&nbsp;</tt></td></tr>
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<td width="100%">Methods defined here:<br>
<dl><dt><a name="MainWindowController-__init__"><strong>__init__</strong></a>(self, model)</dt><dd><tt>Arguments:<br>
-&nbsp;`model`:&nbsp;is&nbsp;a&nbsp;Model&nbsp;<a href="__builtin__.html#object">object</a></tt></dd></dl>

<dl><dt><a name="MainWindowController-draw_coverage"><strong>draw_coverage</strong></a>(self, cog_selection, user_id)</dt><dd><tt>Draw&nbsp;Coverage&nbsp;Frequency<br>
&nbsp;<br>
Arguments:<br>
-&nbsp;`cog_selection`:&nbsp;(cog,&nbsp;file_name)<br>
-&nbsp;`user_id`:&nbsp;user&nbsp;id</tt></dd></dl>

<dl><dt><a name="MainWindowController-draw_function_category"><strong>draw_function_category</strong></a>(self, cog_files, user_id)</dt><dd><tt>Draw&nbsp;function&nbsp;category</tt></dd></dl>

<dl><dt><a name="MainWindowController-draw_segment"><strong>draw_segment</strong></a>(self, cog_selection, user_id)</dt><dd><tt>Draw&nbsp;segment&nbsp;recruitment<br>
Arguments:<br>
-&nbsp;`cog_selection`:(cog_name,&nbsp;file_name)<br>
-&nbsp;`user_id`:&nbsp;user&nbsp;id</tt></dd></dl>

<dl><dt><a name="MainWindowController-draw_similarity_tree"><strong>draw_similarity_tree</strong></a>(self, cog_selection)</dt><dd><tt>Draw&nbsp;the&nbsp;clustering&nbsp;of&nbsp;different&nbsp;communities&nbsp;(datasets)&nbsp;based&nbsp;on<br>
their&nbsp;functional&nbsp;similarity&nbsp;(spearman&nbsp;correlation&nbsp;of&nbsp;the&nbsp;relative&nbsp;abundance<br>
of&nbsp;different&nbsp;COG&nbsp;functions)</tt></dd></dl>

<dl><dt><a name="MainWindowController-get_cogs"><strong>get_cogs</strong></a>(self, cog_selection, user_id)</dt><dd><tt>Return&nbsp;a&nbsp;list&nbsp;of&nbsp;cog&nbsp;<a href="__builtin__.html#object">object</a></tt></dd></dl>

<dl><dt><a name="MainWindowController-get_cogs_with_hitp"><strong>get_cogs_with_hitp</strong></a>(self, cog_selection, user_id)</dt><dd><tt>Return&nbsp;a&nbsp;list&nbsp;of&nbsp;cog&nbsp;<a href="__builtin__.html#object">object</a>&nbsp;and&nbsp;hitp&nbsp;data<br>
cog_selection:&nbsp;is&nbsp;a&nbsp;list&nbsp;of&nbsp;(cog_name,&nbsp;file_name)&nbsp;from&nbsp;UI</tt></dd></dl>

<dl><dt><a name="MainWindowController-get_model"><strong>get_model</strong></a>(self)</dt></dl>

<dl><dt><a name="MainWindowController-load_cog_file"><strong>load_cog_file</strong></a>(self, file_name)</dt><dd><tt>Load&nbsp;cog&nbsp;from&nbsp;file<br>
&nbsp;<br>
Arguments:<br>
-&nbsp;`file_name`:&nbsp;file&nbsp;path</tt></dd></dl>

<dl><dt><a name="MainWindowController-load_data_directory"><strong>load_data_directory</strong></a>(self, directory_name)</dt><dd><tt>Load&nbsp;data&nbsp;files&nbsp;in&nbsp;directory_name</tt></dd></dl>

<dl><dt><a name="MainWindowController-load_data_file"><strong>load_data_file</strong></a>(self, file_name, user_id<font color="#909090">=None</font>)</dt><dd><tt>Load&nbsp;genome&nbsp;data&nbsp;file<br>
&nbsp;<br>
Arguments:<br>
-&nbsp;`file_name`:&nbsp;file&nbsp;path</tt></dd></dl>

<dl><dt><a name="MainWindowController-remove_data_file"><strong>remove_data_file</strong></a>(self, file_name, user_id)</dt><dd><tt>Remove&nbsp;data&nbsp;file&nbsp;from&nbsp;model</tt></dd></dl>

<dl><dt><a name="MainWindowController-set_hitp_folder"><strong>set_hitp_folder</strong></a>(self, path)</dt><dd><tt>Set&nbsp;the&nbsp;hitp&nbsp;data&nbsp;folder<br>
&nbsp;<br>
Arguments:<br>
-&nbsp;`path`:</tt></dd></dl>

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Data and other attributes defined here:<br>
<dl><dt><strong>__dict__</strong> = &lt;dictproxy object&gt;<dd><tt>dictionary&nbsp;for&nbsp;instance&nbsp;variables&nbsp;(if&nbsp;defined)</tt></dl>

<dl><dt><strong>__weakref__</strong> = &lt;attribute '__weakref__' of 'MainWindowController' objects&gt;<dd><tt>list&nbsp;of&nbsp;weak&nbsp;references&nbsp;to&nbsp;the&nbsp;<a href="__builtin__.html#object">object</a>&nbsp;(if&nbsp;defined)</tt></dl>

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<font color="#ffffff" face="helvetica, arial"><big><strong>Data</strong></big></font></td></tr>
    
<tr><td bgcolor="#55aa55"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><strong>__author__</strong> = 'Lei Chen &lt;hide1713@gmail.com&gt;'</td></tr></table><p>
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<font color="#ffffff" face="helvetica, arial"><big><strong>Author</strong></big></font></td></tr>
    
<tr><td bgcolor="#7799ee"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%">Lei&nbsp;Chen&nbsp;&lt;hide1713@gmail.com&gt;</td></tr></table>
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